PQN and DQN: Algorithms for expression microarrays

Journal of Theoretical Biology

Volumn 243, Issue 2, 2006, Pages 273-278

  Liu, Wei min ^a   Li, Rui ^a   Sun, James Z ^a   Wang, Jing ^a   Tsai, Julie ^a   Wen, Wei ^a   Kohlmann, Alexander ^a   Mickey Williams, P ^a  

^a ROCHE MOLECULAR SYSTEMS   (United States)

Author keywords

Gene expression; Hybridization; Microarray; Normalization; Robustness

Indexed keywords

GENE EXPRESSION; GENETIC ALGORITHM; PROBE;

ANALYTICAL ERROR; AREA UNDER THE CURVE; ARTICLE; ASSAY; BIOINFORMATICS; DATA ANALYSIS; GENETIC ALGORITHM; MATHEMATICAL COMPUTING; MICROARRAY ANALYSIS; PRIORITY JOURNAL; RECEIVER OPERATING CHARACTERISTIC; THEORETICAL MODEL;

ALGORITHMS; ANIMALS; AREA UNDER CURVE; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ROC CURVE;

EID: 33749620427     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2006.06.017     Document Type: Article

References (19)

1. Affymetrix. Guide to Probe Logarithmic Intensity Error Estimation (PLIER) (2003), Affymetrix, Santa Clara
2. Bolstad B.M., Irizarry R.A., Astrand M., and Speed T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19 (2003) 185-193
3. Chou K.-C. Structural bioinformatics and its impact to biomedical science. Current Medicinal Chemistry 11 (2004) 2105-2134
4. Cope L.M., Irizarry R.A., Jaffee H.A., Wu Z., and Speed T.P. A benchmark for Affymetrix GeneChip expression measures. Bioinformatics 20 (2004) 323-331
5. Di X., Matsuzaki H., Webster T.A., Hubbell E., Liu G., Dong S., Bartell D., Huang J., Chiles R., Yang G., Shen M., Kulp D., Kennedy G.C., Mei R., Jones K.W., and Cawley S. Dynamic model based algorithms for screening and genotyping over 100 K SNPs on oligonucleotide microarrays. Bioinformatics 21 (2005) 1958-1963
6. Fodor S.P., Read J.L., Pirrung M.C., Stryer L., Lu A.T., and Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science 251 (1991) 767-773
7. Green D.M., and Swets J.A. Signal Detection Theory and Psychophysics (1966), Wiley, New York
8. Hu G.K., Madore S.J., Moldover B., Jatkoe T., Balaban D., Thomas J., and Wang Y.X. Predicting splice variant from DNA chip expression data. Genome Res. 11 (2001) 1237-1245
9. Hubbell, E., 2003. Some M-estimates for expression analysis. Affymetrix GeneChip microarray low-level workshop. http://www.affymetrix.com.
10. Hubbell E., Liu W.-m., and Mei R. Robust estimators for expression analysis. Bioinformatics 18 (2002) 1585-1592
11. Irizarry R.A., Bolstad B.M., Collin F., Cope L.M., Hobbs B., and Speed T.P. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31 (2003) 1-8 10.1093/nar/gng015
12. Irizarry R.A., Hobbs B., Collin F., Beazer-Barclay Y.D., Antonellis K.J., Scherf U., and Speed T.P. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4 (2003) 249-264
13. Kennedy G.C., Matsuzaki H., Dong S., Liu W.-m., Huang J., Liu G., Su X., Cao M., Chen W., Zhang J., Liu W., Yang G., Di X., Ryder T., He Z., Surti U., Phillips M.S., Boyce-Jacino M.T., Fodor S.P.A., and Jones K.W. Large scale genotyping of complex DNA. Nat. Biotechnol. 21 (2003) 1233-1237
14. Li C., and Wong W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl Acad. Sci. USA 98 (2001) 31-36
15. Li C., and Wong W.H. Model-based analysis of oligonucleotide arrays: model validation design issues and standard error applications. Genome Biol. 2 8 (2001) Research 0032.1-0032.11
16. Lockhart D.J., Dong H., Byrne M.C., Follettie M.T., Gallo M.V., Chee M.S., Mittmann M., Wang C., Kobayashi M., Horton H., and Brown E.L. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14 (1996) 1675-1680
17. Rosenberger J.L., and Gasko M. Comparing location estimators: trimmed means, medians, and trimean. In: Hoaglin H.C., Mosteller F., and Tukey J.W. (Eds). Understanding Robust and Exploratory Data Analysis (1983), Wiley, New York 297-338
18. Swets J.A., and Pickett R.M. Evaluation of Diagnostic Systems: Methods from Signal Detection Theory (1982), Academic Press, New York
19. Wu Z., Irizarry R.A., Gentleman R., Martinez-Murillo F., and Spencer F. A model-based background adjustment for oligonucleotide expression arrays. J. Amer. Stat. Assoc. 99 (2004) 909-917